cis element/transcription factor analysis (cis/TF): A method for discovering transcription factor/cis element relationships

We report a simple new algorithm, cis/TF, that uses genomewide expression d ata and the full genomic sequence to match transcription factors to their b inding sites. Most previous computational methods discovered binding sites by clustering genes having similar expression patterns and then identifying over-represented Subsequences in the promoter regions of those genes. By c ontrast, cis/TF asserts that B is a likely binding site of a transcription factor T if the expression pattern of T is correlated to the composite expr ession patterns of all genes containing B, even when those genes are not mu tually correlated. Thus, our method focuses on binding sites rather than ge nes. The algorithm has successfully identified experimentally-supported tra nscription factor binding relationships in tests on several data sets from Saccharomyces cerevisiae.